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Unit test failure on i386 #238

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avalentino opened this issue Sep 7, 2019 · 4 comments
Closed

Unit test failure on i386 #238

avalentino opened this issue Sep 7, 2019 · 4 comments

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@avalentino
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Unit tests seems to fail on i386 with Python 3.7 for PySPH v1.0a6.

Th test has been run using the following command:

$ python3.7 -m pytest -k 'not test_sph_evaluator and not TestInterpolator'

Test resulst are reported below:

============================= test session starts ==============================
platform linux -- Python 3.7.4+, pytest-4.6.5, py-1.8.0, pluggy-0.12.0
rootdir: /<<PKGBUILDDIR>>, inifile: tox.ini
collected 1034 items / 71 deselected / 963 selected

pysph/base/tests/test_carray.py ........................                 [  2%]
pysph/base/tests/test_device_helper.py .ss.ss.ss.ss.ss.ss.ss.ss.ss.ss.ss [  5%]
FssFss.ss.ss.ssFss                                                       [  7%]
pysph/base/tests/test_domain_manager.py .........                        [  8%]
pysph/base/tests/test_kernel.py ........................................ [ 12%]
.................................................................        [ 19%]
pysph/base/tests/test_linalg3.py .......                                 [ 20%]
pysph/base/tests/test_neighbor_cache.py ...                              [ 20%]
pysph/base/tests/test_nnps.py .......ssssssssss......................... [ 25%]
....................................................ssssssssssssssssssss [ 32%]
sssssssssssssssssssssssssssssssssssssssssss............................. [ 39%]
...................                                                      [ 41%]
pysph/base/tests/test_octree.py .....s...s...s...s...s...s...s...s.      [ 45%]
pysph/base/tests/test_particle_array.py ..............................ss [ 48%]
ssssssssssssssssssssssssssssssssssssssssssssssssss                       [ 54%]
pysph/base/tests/test_periodic_nnps.py ...........                       [ 55%]
pysph/base/tests/test_reduce_array.py ......                             [ 55%]
pysph/cpy/tests/test_array.py .ss.ss.ss.ss.ss.ss.ss.ss.ss.ss.ss.ss       [ 59%]
pysph/cpy/tests/test_ast_utils.py .......                                [ 60%]
pysph/cpy/tests/test_capture_stream.py .....                             [ 60%]
pysph/cpy/tests/test_config.py ............                              [ 62%]
pysph/cpy/tests/test_cython_generator.py ...............                 [ 63%]
pysph/cpy/tests/test_ext_module.py .......                               [ 64%]
pysph/cpy/tests/test_jit.py .................                            [ 66%]
pysph/cpy/tests/test_low_level.py ssss..                                 [ 66%]
pysph/cpy/tests/test_parallel.py s.ss.ss.ss.ss.ss.ss..ss..ss..ss..ss.ss. [ 70%]
ss.ss.ss.ss.ss..ss..ss..ss..s                                            [ 73%]
pysph/cpy/tests/test_translator.py ..................................... [ 77%]
............                                                             [ 78%]
pysph/cpy/tests/test_transpiler.py ..                                    [ 79%]
pysph/cpy/tests/test_types.py .......                                    [ 79%]
pysph/examples/tests/test_riemann_solver.py s........                    [ 80%]
pysph/parallel/tests/test_openmp.py .                                    [ 80%]
pysph/parallel/tests/test_parallel.py ssssss                             [ 81%]
pysph/parallel/tests/test_parallel_run.py s                              [ 81%]
pysph/solver/tests/test_application.py ..                                [ 81%]
pysph/solver/tests/test_solver.py ..                                     [ 82%]
pysph/solver/tests/test_solver_utils.py ......sssss.                     [ 83%]
pysph/sph/tests/test_acceleration_eval.py ....................ssssssssss [ 86%]
ssssssssssssssssss                                                       [ 88%]
pysph/sph/tests/test_acceleration_eval_cython_helper.py ...              [ 88%]
pysph/sph/tests/test_equations.py ...............                        [ 90%]
pysph/sph/tests/test_integrator.py .........sss                          [ 91%]
pysph/sph/tests/test_integrator_cython_helper.py .                       [ 91%]
pysph/sph/tests/test_integrator_step.py ..                               [ 91%]
pysph/sph/tests/test_kernel_corrections.py ................              [ 93%]
pysph/sph/tests/test_linalg.py ...........                               [ 94%]
pysph/sph/tests/test_multi_group_integrator.py .s                        [ 94%]
pysph/sph/tests/test_riemann_solver.py .............                     [ 96%]
pysph/sph/tests/test_scheme.py .                                         [ 96%]
pysph/sph/tests/test_simple_inlet_outlet.py .......                      [ 96%]
pysph/tools/tests/test_geometry.py .............s...                     [ 98%]
pysph/tools/tests/test_geometry_stl.py .....F..                          [ 99%]
pysph/tools/tests/test_interpolator.py ...                               [ 99%]
pyzoltan/core/tests/test_zoltan.py ss                                    [100%]

=================================== FAILURES ===================================
________________ TestDeviceHelper.test_remove_particles[cython] ________________

obj = array([         0,          0,   -2097152, 1106247679], dtype=int32)
method = 'take', args = (array([0, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}

    def _wrapfunc(obj, method, *args, **kwds):
        try:
>           return getattr(obj, method)(*args, **kwds)
E           TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:56: TypeError

During handling of the above exception, another exception occurred:

self = <pysph.base.tests.test_device_helper.TestDeviceHelper object at 0xf38632ac>
backend = 'cython'

    @test_all_backends
    def test_remove_particles(self, backend):
        check_import(backend)
        self.setup()
        # Given
        pa = self.pa
        h = DeviceHelper(pa, backend=backend)
    
        # When
        pa.set_device_helper(h)
        h.resize(4)
        h.x.set(np.array([2.0, 3.0, 4.0, 5.0], h.x.dtype))
    
        indices = np.array([1, 2], dtype=np.uint32)
        indices = array.to_device(indices, backend=backend)
    
>       h.remove_particles(indices)

pysph/base/tests/test_device_helper.py:289: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysph/base/device_helper.py:400: in remove_particles
    self._remove_particles_bool(if_remove)
pysph/base/device_helper.py:343: in _remove_particles_bool
    self._data[prop].align(s_index)
pysph/cpy/array.py:440: in align
    backend=self.backend))
pysph/cpy/array.py:220: in take
    out = np.take(ary.dev, indices.dev)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:189: in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:66: in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

obj = array([         0,          0,   -2097152, 1106247679], dtype=int32)
method = 'take', args = (array([0, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}
wrap = <built-in method __array_wrap__ of numpy.ndarray object at 0xf20d5278>

    def _wrapit(obj, method, *args, **kwds):
        try:
            wrap = obj.__array_wrap__
        except AttributeError:
            wrap = None
>       result = getattr(asarray(obj), method)(*args, **kwds)
E       TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:46: TypeError
----------------------------- Captured stdout call -----------------------------
Compiling code at: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.pyx
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.cpp
building 'm_9195542b3857fa6f3b64c7d14cb67f62' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/lib.linux-i386-3.7/m_9195542b3857fa6f3b64c7d14cb67f62.cpython-37m-i386-linux-gnu.so -fopenmp
Compiling code at: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.pyx
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.cpp
building 'm_2250e3389bc8cd7df0c03bbb346401c7' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/lib.linux-i386-3.7/m_2250e3389bc8cd7df0c03bbb346401c7.cpython-37m-i386-linux-gnu.so -fopenmp
Compiling code at: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.pyx
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.cpp
building 'm_5cf03441ed5cac9d4491b85306d9754c' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/lib.linux-i386-3.7/m_5cf03441ed5cac9d4491b85306d9754c.cpython-37m-i386-linux-gnu.so -fopenmp
____________ TestDeviceHelper.test_remove_tagged_particles[cython] _____________

obj = array([0, 0, 1, 0, 1], dtype=int32), method = 'take'
args = (array([0, 1, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}

    def _wrapfunc(obj, method, *args, **kwds):
        try:
>           return getattr(obj, method)(*args, **kwds)
E           TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:56: TypeError

During handling of the above exception, another exception occurred:

self = <pysph.base.tests.test_device_helper.TestDeviceHelper object at 0xf2fa328c>
backend = 'cython'

    @test_all_backends
    def test_remove_tagged_particles(self, backend):
        check_import(backend)
        self.setup()
        # Given
        pa = self.pa
        h = DeviceHelper(pa, backend=backend)
    
        # When
        pa.set_device_helper(h)
        h.resize(5)
        h.x.set(np.array([2.0, 3.0, 4.0, 5.0, 6.0], h.x.dtype))
        h.tag.set(np.array([0, 0, 1, 0, 1], h.tag.dtype))
    
>       h.remove_tagged_particles(1)

pysph/base/tests/test_device_helper.py:308: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysph/base/device_helper.py:415: in remove_tagged_particles
    self._remove_particles_bool(if_remove)
pysph/base/device_helper.py:343: in _remove_particles_bool
    self._data[prop].align(s_index)
pysph/cpy/array.py:440: in align
    backend=self.backend))
pysph/cpy/array.py:220: in take
    out = np.take(ary.dev, indices.dev)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:189: in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:66: in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

obj = array([0, 0, 1, 0, 1], dtype=int32), method = 'take'
args = (array([0, 1, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}
wrap = <built-in method __array_wrap__ of numpy.ndarray object at 0xf27ff3b8>

    def _wrapit(obj, method, *args, **kwds):
        try:
            wrap = obj.__array_wrap__
        except AttributeError:
            wrap = None
>       result = getattr(asarray(obj), method)(*args, **kwds)
E       TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:46: TypeError
----------------------------- Captured stdout call -----------------------------
Precompiled code from: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.pyx
Precompiled code from: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.pyx
_______________ TestDeviceHelper.test_extract_particles[cython] ________________

obj = array([0, 0, 0, 0], dtype=int32), method = 'take'
args = (array([1, 2], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}

    def _wrapfunc(obj, method, *args, **kwds):
        try:
>           return getattr(obj, method)(*args, **kwds)
E           TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:56: TypeError

During handling of the above exception, another exception occurred:

self = <pysph.base.tests.test_device_helper.TestDeviceHelper object at 0xf25e82ac>
backend = 'cython'

    @test_all_backends
    def test_extract_particles(self, backend):
        check_import(backend)
        self.setup()
        # Given
        pa = get_particle_array(name='f', x=[0.0, 1.0, 2.0, 3.0],
                                m=1.0, rho=2.0)
        h = DeviceHelper(pa, backend=backend)
        pa.set_device_helper(h)
    
        # When
        indices = np.array([1, 2], dtype=np.uint32)
        indices = array.to_device(indices, backend=backend)
    
>       result_pa = h.extract_particles(indices)

pysph/base/tests/test_device_helper.py:376: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysph/base/device_helper.py:584: in extract_particles
    backend=self.backend))
pysph/cpy/array.py:220: in take
    out = np.take(ary.dev, indices.dev)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:189: in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:66: in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

obj = array([0, 0, 0, 0], dtype=int32), method = 'take'
args = (array([1, 2], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': None}
wrap = <built-in method __array_wrap__ of numpy.ndarray object at 0xf2c50570>

    def _wrapit(obj, method, *args, **kwds):
        try:
            wrap = obj.__array_wrap__
        except AttributeError:
            wrap = None
>       result = getattr(asarray(obj), method)(*args, **kwds)
E       TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:46: TypeError
----------------------------- Captured stdout call -----------------------------
Compiling code at: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.pyx
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.cpp
building 'm_d34793424e1f2e13e0fecd1771d2a7c0' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/temp.linux-i386-3.7/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/build/lib.linux-i386-3.7/m_d34793424e1f2e13e0fecd1771d2a7c0.cpython-37m-i386-linux-gnu.so -fopenmp
______________________ TestGeometry.test_get_stl_surface _______________________

self = <pysph.tools.tests.test_geometry_stl.TestGeometry testMethod=test_get_stl_surface>

    def test_get_stl_surface(self):
        """Check if stl surface is generated correctly for unit cube"""
        cube_fname = self._generate_cube_stl()
        h = 0.1
        x, y, z = G.get_stl_surface(cube_fname, h, h, 1)
>       self._cube_assert(x, y, z, h)

pysph/tools/tests/test_geometry_stl.py:176: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pysph.tools.tests.test_geometry_stl.TestGeometry testMethod=test_get_stl_surface>
x = array([0., 0., 0., ..., 1., 1., 1.])
y = array([-0.1, -0.1, -0.1, ...,  1. ,  1. ,  1. ])
z = array([0. , 0.1, 0.2, ..., 0.8, 0.9, 1. ]), h = 0.1

    def _cube_assert(self, x, y, z, h):
        """Check if x,y,z lie within surface of thickness `h` of a unit cube"""
        def surface1(x, y, z): return min(abs(x), abs(1 - x)) < h and \
            y > -h and y < 1 + h and z > -h and z < 1 + h
    
        def on_surface(x, y, z): return surface1(x, y, z) or \
            surface1(y, x, z) or surface1(z, x, y)
    
        for i in range(x.shape[0]):
>           assert on_surface(x[i], y[i], z[i])
E           AssertionError: assert False
E            +  where False = <function TestGeometry._cube_assert.<locals>.on_surface at 0xf20b2fa4>(0.0, -0.1, 0.0)

pysph/tools/tests/test_geometry_stl.py:162: AssertionError
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:242
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:242
  /usr/lib/python3/dist-packages/_pytest/mark/structures.py:242: PytestCollectionWarning: cannot collect 'test_all_backends' because it is not a function.
    def __call__(self, *args, **kwargs):

/usr/lib/python3/dist-packages/_pytest/mark/structures.py:334
  /usr/lib/python3/dist-packages/_pytest/mark/structures.py:334: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    PytestUnknownMarkWarning,

/usr/lib/python3/dist-packages/_pytest/mark/structures.py:334
  /usr/lib/python3/dist-packages/_pytest/mark/structures.py:334: PytestUnknownMarkWarning: Unknown pytest.mark.parallel - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/latest/mark.html
    PytestUnknownMarkWarning,

.pybuild/cpython3_3.7/build/pysph/base/tests/test_device_helper.py::TestDeviceHelper::test_get_number_of_particles[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_91e0575b640469ac68a80641e2db24b0.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_device_helper.py::TestDeviceHelper::test_remove_particles[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9195542b3857fa6f3b64c7d14cb67f62.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_device_helper.py::TestDeviceHelper::test_remove_particles[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_2250e3389bc8cd7df0c03bbb346401c7.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_device_helper.py::TestDeviceHelper::test_remove_particles[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5cf03441ed5cac9d4491b85306d9754c.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_device_helper.py::TestDeviceHelper::test_extract_particles[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d34793424e1f2e13e0fecd1771d2a7c0.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestOctreeFor1DDataset::test_levels_in_tree
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestOctreeFor1DDataset::test_parent_for_node
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestOctreeFor1DDataset::test_plot_root
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestOctreeFor1DDataset::test_sum_of_indices_lengths_equals_total_number_of_particles
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py:192: DeprecationWarning: object of type <class 'float'> cannot be safely interpreted as an integer.
    self.x = np.linspace(0, 1, num=N)

.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestCompressedOctreeFor1DDataset::test_levels_in_tree
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestCompressedOctreeFor1DDataset::test_parent_for_node
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestCompressedOctreeFor1DDataset::test_plot_root
.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py::TestCompressedOctreeFor1DDataset::test_sum_of_indices_lengths_equals_total_number_of_particles
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/base/tests/test_octree.py:238: DeprecationWarning: object of type <class 'float'> cannot be safely interpreted as an integer.
    self.x = np.linspace(0, 1, num=N)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_array.py::test_remove[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_54f9f75e0f45f43dc44f58b838c92f06.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_array.py::test_remove[cython]
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_70edfcc8cb29a9c84af9920f87d1b951.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_ext_module.py::TestExtModule::test_load_module
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/tmp8655ndf6/m_59a539f0f96ecda080392b137f7ab38e.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_ext_module.py::TestExtModule::test_rebuild_when_dependencies_change
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/tmp0sb88tdv/m_59a539f0f96ecda080392b137f7ab38e.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_jit.py::TestAnnotationHelper::test_non_jit_call_as_call_arg
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/cpy/jit.py:125: UserWarning: 
  In code in line 5:
  
      return g(sin(a))
               ^
  
  
  Function called is not marked by the annotate decorator. Argument
  type defaulting to 'double'. If the type is not 'double', store
  the value in a variable of appropriate type and use the variable
  
    warnings.warn(msg)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_jit.py::TestAnnotationHelper::test_non_jit_call_in_return
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/cpy/jit.py:125: UserWarning: 
  In code in line 5:
  
      return sin(a)
             ^
  
  
  Function called is not marked by the annotate decorator. Argument
  type defaulting to 'double'. If the type is not 'double', store
  the value in a variable of appropriate type and use the variable
  
    warnings.warn(msg)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_low_level.py::TestCython::test_cython_code_with_return_and_nested_call
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_74d45969c7f812097ca91e32d292c9b5.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_low_level.py::TestCython::test_cython_with_externs
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_d99220a885a6ea16f2900812b6af8d9c.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_elementwise_works_with_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_7e50ca36a38cc6e5bdb25fdd039133ca.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_reduction_works_neutral_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9a2c7ebf648842a29b3befe6f44f4a0e.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_reduction_works_with_external_func_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_3913705ba17110bad123d7fec52d1fa6.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_reduction_works_with_map_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_ea8309077f21b49c2e55c4fff007c57d.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_reduction_works_without_map_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_159c0a504e13152c82e3025f68c52a97.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_scan_last_item_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9c51f8a3ca12ef2fff590c265f372100.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_scan_works_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_17aa11b78980ae118499ef3b67528262.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_scan_works_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_21c9822c18457511d7d6c48f60636280.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_scan_works_with_external_func_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_303d8bc784c0fe041df30586ae859245.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_scan_works_with_external_func_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_116d33965d4a335e1a3a722a1aa511aa.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_segmented_scan_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_678b9adc1c242c435c53cf38d505d0ea.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_segmented_scan_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9824ea52a3de157665153f82c134736f.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_unique_scan_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_10cce52efb3dc468ae85f83fe5c9ea40.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtils::test_unique_scan_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_c5d750f49c73249649bcbfb5023e25d4.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtilsJIT::test_reduction_works_with_external_func_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5662c6866ef7f5d806bb92c47362ed37.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtilsJIT::test_reduction_works_with_map_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_5c107ae13a11a41f9f03e8f69b3ce2c5.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtilsJIT::test_scan_works_with_external_func_cython
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_9c2467add4a88d72ce0a1f3a67fb447c.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/cpy/tests/test_parallel.py::TestParallelUtilsJIT::test_scan_works_with_external_func_cython_parallel
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.cpy/source/py3.7-linux-i386/m_3ce863393ce97030d92dd85a8bb3e38d.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_initialize_pair
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_1ca2f6f3c87a0aced1147a42323c9e0b.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_pre_post_functions_in_group
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_380d33049e60eeba93e7e250e099d136.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_call_py_initialize
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_cc7e6f6747bcab4616b25771b58a0003.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_handle_repeated_helper_functions
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_605c1c7cab1f607d6ddbe4596f54170c.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_iterate_iterated_group
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_e6c3637f476bcecde9ab79fac8a493bc.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_iterate_nested_groups
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_2c18826a975a61c409256394bf7c334c.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_not_iterate_normal_group
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_b8d4d327d2a1ea45d3cd9acaaeb31eae.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_run_reduce
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_866e76262ba81f9c5715e8ded2fe3a59.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_constants
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_a39281cc879a9b6273edcdbed96961e2.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_loop_all_and_loop
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_6602b7587dbde3a4a1b3e89c9c525b5d.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_support_loop_all_and_loop
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_e689702faaab40fa4ea1f65ea53a7bef.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_acceleration_eval.py::TestAccelerationEval1D::test_should_work_with_non_double_arrays
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_eb65dab7322c93aca79da89ad850753b.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_only_py_when_no_stage
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_0f8ccecffa92800f1e1c60caf7d61af8.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_py_stage1
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_128d15c2d9e0ca930a88ca79cf433a70.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_integrator_calls_py_stage1_stage2
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_bb0974af10f5bc3963019f23b881db5f.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_integrator.py::TestLeapFrogIntegrator::test_leapfrog
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_9eceb868e252ed6a0ece6395929a8bcb.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_integrator.py::TestPEFRLIntegrator::test_pefrl
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_172dfa9e1631ea7d9482824bc06d14ec.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_crksph
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_f24545a9be7b831ac0425b878177cb20.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_crksph_symmetric
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_437e8cc88a6fd6e3c098b821810973a7.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_gradient_correction
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_6606a5783a6859b7a65db9ef38136431.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_kernel_corrections.py::TestKernelCorrection2D::test_mixed_gradient_correction
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_25d6e5546a9f5073e1f4f91086e35c77.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:63: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:64: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_band_matrix
.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
.pybuild/cpython3_3.7/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
.pybuild/cpython3_3.7/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
  /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:71: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return matrix(data, dtype=dtype, copy=False)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:74: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_dense_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:75: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:52: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_general_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:53: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:97: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:98: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:109: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_symmetric_positivedefinite_Matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:110: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:86: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    mat = np.matrix(mat)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py::TestLinalg::test_tridiagonal_matrix
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/sph/tests/test_linalg.py:87: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    new_b = mat * np.transpose(np.matrix(result))

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_multi_group_integrator.py::TestMultiGroupIntegrator::test_different_accels_per_integrator
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_b02855c53973b41cd416728f4f3d5a63.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/sph/tests/test_multi_group_integrator.py::TestMultiGroupIntegrator::test_different_accels_per_integrator
  /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/.pysph/source/py3.7-linux-i386/m_646dd531e33008b11fdce652ba19a184.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython3_3.7/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/tools/geometry.py:176: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    rotation_matrix = matrix_exp(np.matrix(matrix))

.pybuild/cpython3_3.7/build/pysph/tools/tests/test_geometry.py::TestGeometry::test_rotate
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7/build/pysph/tools/tests/test_geometry.py:76: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    rotation_matrix = G.matrix_exp(np.matrix(mat))

-- Docs: https://docs.pytest.org/en/latest/warnings.html

= 4 failed, 676 passed, 283 skipped, 71 deselected, 88 warnings in 626.70 seconds =

More detail are available in [1].

[1] https://buildd.debian.org/status/fetch.php?pkg=pysph&arch=i386&ver=1.0%7Ea6-3&stamp=1567841029&raw=0
@avalentino
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After the update to the latest git revision (e3d5e10) there are still 2 test failures:

============================= test session starts ==============================
platform linux -- Python 3.8.1, pytest-4.6.8, py-1.8.0, pluggy-0.13.0
rootdir: /<<PKGBUILDDIR>>, inifile: tox.ini
collected 889 items / 90 deselected / 799 selected

pysph/base/tests/test_device_helper.py .ss.ss.ss.ss.ss.ss.ss.ss.ss.ss.ss [  4%]
FssFss.ss.ss.ss.ss.sss                                                   [  6%]
pysph/base/tests/test_domain_manager.py sss.........                     [  8%]
pysph/base/tests/test_kernel.py ........................................ [ 13%]
.................................................................        [ 21%]
pysph/base/tests/test_linalg3.py .......                                 [ 22%]
pysph/base/tests/test_neighbor_cache.py ....                             [ 22%]
pysph/base/tests/test_nnps.py .......ssssssssss......................... [ 28%]
....................................................ssssssssssssssssssss [ 37%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss........ [ 46%]
.........................................                                [ 51%]
pysph/base/tests/test_octree.py .....s...s...s...s...s...s...s...s.      [ 55%]
pysph/base/tests/test_particle_array.py ................................ [ 59%]
...ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss        [ 67%]
pysph/base/tests/test_periodic_nnps.py ............                      [ 69%]
pysph/base/tests/test_reduce_array.py ......                             [ 70%]
pysph/base/tests/test_utils.py ..                                        [ 70%]
pysph/examples/tests/test_riemann_solver.py s........                    [ 71%]
pysph/parallel/tests/test_openmp.py .                                    [ 71%]
pysph/parallel/tests/test_parallel.py ssssss                             [ 72%]
pysph/parallel/tests/test_parallel_run.py s                              [ 72%]
pysph/solver/tests/test_application.py ...                               [ 72%]
pysph/solver/tests/test_solver.py ..                                     [ 73%]
pysph/solver/tests/test_solver_utils.py ......sssss.                     [ 74%]
pysph/sph/bc/tests/test_simple_inlet_outlet.py .......                   [ 75%]
pysph/sph/tests/test_acceleration_eval.py ....................ssssssssss [ 79%]
ssssssssssssssssssssssssssssssssssssssssssssss                           [ 84%]
pysph/sph/tests/test_acceleration_eval_cython_helper.py ...              [ 85%]
pysph/sph/tests/test_equations.py ...............                        [ 87%]
pysph/sph/tests/test_integrator.py ...............ssssssss               [ 90%]
pysph/sph/tests/test_integrator_cython_helper.py .                       [ 90%]
pysph/sph/tests/test_integrator_step.py ..                               [ 90%]
pysph/sph/tests/test_kernel_corrections.py ................              [ 92%]
pysph/sph/tests/test_linalg.py .............                             [ 94%]
pysph/sph/tests/test_multi_group_integrator.py .s                        [ 94%]
pysph/sph/tests/test_riemann_solver.py .............                     [ 95%]
pysph/sph/tests/test_scheme.py .                                         [ 96%]
pysph/tools/tests/test_geometry.py .............s...                     [ 98%]
pysph/tools/tests/test_geometry_stl.py ...........                       [ 99%]
pysph/tools/tests/test_interpolator.py ...                               [100%]

=================================== FAILURES ===================================
________________ TestDeviceHelper.test_remove_particles[cython] ________________

obj = array([         0,          0,   -2097152, 1106247679], dtype=int32)
method = 'take', args = (array([0, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': array([0, 0], dtype=int32)}
bound = <built-in method take of numpy.ndarray object at 0xf23e2958>

    def _wrapfunc(obj, method, *args, **kwds):
        bound = getattr(obj, method, None)
        if bound is None:
            return _wrapit(obj, method, *args, **kwds)
    
        try:
>           return bound(*args, **kwds)
E           TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:61: TypeError

During handling of the above exception, another exception occurred:

self = <pysph.base.tests.test_device_helper.TestDeviceHelper object at 0xf246b688>
backend = 'cython'

    @test_all_backends
    def test_remove_particles(self, backend):
        check_import(backend)
        self.setup()
        # Given
        pa = self.pa
        h = DeviceHelper(pa, backend=backend)
    
        # When
        pa.set_device_helper(h)
        h.resize(4)
        h.x.set(np.array([2.0, 3.0, 4.0, 5.0], h.x.dtype))
    
        indices = np.array([1, 2], dtype=np.uint32)
        indices = array.to_device(indices, backend=backend)
    
>       h.remove_particles(indices)

pysph/base/tests/test_device_helper.py:295: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysph/base/device_helper.py:446: in remove_particles
    self._remove_particles_bool(if_remove, align=align)
pysph/base/device_helper.py:405: in _remove_particles_bool
    self._data[prop] = self._data[prop].align(s_index)
/usr/lib/python3/dist-packages/compyle/array.py:887: in align
    return take(self, indices, backend=self.backend, out=out)
/usr/lib/python3/dist-packages/compyle/array.py:563: in take
    np.take(ary.dev, indices.dev, out=out.dev)
<__array_function__ internals>:5: in take
    ???
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:194: in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:70: in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

obj = array([         0,          0,   -2097152, 1106247679], dtype=int32)
method = 'take', args = (array([0, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': array([0, 0], dtype=int32)}
wrap = <built-in method __array_wrap__ of numpy.ndarray object at 0xf23e2958>

    def _wrapit(obj, method, *args, **kwds):
        try:
            wrap = obj.__array_wrap__
        except AttributeError:
            wrap = None
>       result = getattr(asarray(obj), method)(*args, **kwds)
E       TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:47: TypeError
----------------------------- Captured stdout call -----------------------------
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_ce49303592cccc0f47d12e62e446115e.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_ce49303592cccc0f47d12e62e446115e.cpp
building 'm_ce49303592cccc0f47d12e62e446115e' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/local/include -I/usr/include/python3.8 -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_ce49303592cccc0f47d12e62e446115e.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_ce49303592cccc0f47d12e62e446115e.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_ce49303592cccc0f47d12e62e446115e.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/lib.linux-i386-3.8/m_ce49303592cccc0f47d12e62e446115e.cpython-38-i386-linux-gnu.so -fopenmp
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_bd6d6a8ab7b1792aab85d10bcb603670.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_bd6d6a8ab7b1792aab85d10bcb603670.cpp
building 'm_bd6d6a8ab7b1792aab85d10bcb603670' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/local/include -I/usr/include/python3.8 -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_bd6d6a8ab7b1792aab85d10bcb603670.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_bd6d6a8ab7b1792aab85d10bcb603670.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_bd6d6a8ab7b1792aab85d10bcb603670.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/lib.linux-i386-3.8/m_bd6d6a8ab7b1792aab85d10bcb603670.cpython-38-i386-linux-gnu.so -fopenmp
running build_ext
cythoning /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_5df2595d151df615d925d6d92dc9c48e.pyx to /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_5df2595d151df615d925d6d92dc9c48e.cpp
building 'm_5df2595d151df615d925d6d92dc9c48e' extension
i686-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/local/include -I/usr/include/python3.8 -c /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_5df2595d151df615d925d6d92dc9c48e.cpp -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_5df2595d151df615d925d6d92dc9c48e.o -fopenmp
i686-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/temp.linux-i386-3.8/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/m_5df2595d151df615d925d6d92dc9c48e.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/.compyle/source/py3.8-linux-i386/build/lib.linux-i386-3.8/m_5df2595d151df615d925d6d92dc9c48e.cpython-38-i386-linux-gnu.so -fopenmp
____________ TestDeviceHelper.test_remove_tagged_particles[cython] _____________

obj = array([0, 0, 1, 0, 1], dtype=int32), method = 'take'
args = (array([0, 1, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': array([ 1262746869, -2117160148,   925122456], dtype=int32)}
bound = <built-in method take of numpy.ndarray object at 0xf2cc9728>

    def _wrapfunc(obj, method, *args, **kwds):
        bound = getattr(obj, method, None)
        if bound is None:
            return _wrapit(obj, method, *args, **kwds)
    
        try:
>           return bound(*args, **kwds)
E           TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:61: TypeError

During handling of the above exception, another exception occurred:

self = <pysph.base.tests.test_device_helper.TestDeviceHelper object at 0xf29d9370>
backend = 'cython'

    @test_all_backends
    def test_remove_tagged_particles(self, backend):
        check_import(backend)
        self.setup()
        # Given
        pa = self.pa
        h = DeviceHelper(pa, backend=backend)
    
        # When
        pa.set_device_helper(h)
        h.resize(5)
        h.x.set(np.array([2.0, 3.0, 4.0, 5.0, 6.0], h.x.dtype))
        h.tag.set(np.array([0, 0, 1, 0, 1], h.tag.dtype))
    
>       h.remove_tagged_particles(1)

pysph/base/tests/test_device_helper.py:314: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysph/base/device_helper.py:461: in remove_tagged_particles
    self._remove_particles_bool(if_remove, align=align)
pysph/base/device_helper.py:405: in _remove_particles_bool
    self._data[prop] = self._data[prop].align(s_index)
/usr/lib/python3/dist-packages/compyle/array.py:887: in align
    return take(self, indices, backend=self.backend, out=out)
/usr/lib/python3/dist-packages/compyle/array.py:563: in take
    np.take(ary.dev, indices.dev, out=out.dev)
<__array_function__ internals>:5: in take
    ???
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:194: in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:70: in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

obj = array([0, 0, 1, 0, 1], dtype=int32), method = 'take'
args = (array([0, 1, 3], dtype=uint32),)
kwds = {'axis': None, 'mode': 'raise', 'out': array([ 1262746869, -2117160148,   925122456], dtype=int32)}
wrap = <built-in method __array_wrap__ of numpy.ndarray object at 0xf2cc9728>

    def _wrapit(obj, method, *args, **kwds):
        try:
            wrap = obj.__array_wrap__
        except AttributeError:
            wrap = None
>       result = getattr(asarray(obj), method)(*args, **kwds)
E       TypeError: Cannot cast array data from dtype('uint32') to dtype('int32') according to the rule 'safe'

/usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:47: TypeError

= 2 failed, 514 passed, 283 skipped, 90 deselected, 64 warnings in 361.13 seconds =

@prabhuramachandran
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@adityapb -- would it be possible to take a quick look?

@prabhuramachandran
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@avalentino -- is this still broken?

@avalentino
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@prabhuramachandran it works now.
Please feel free to close this issue

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@prabhuramachandran @avalentino